TY - JOUR
T1 - Analysis of somatic microsatellite indels identifies driver events in human tumors
AU - Maruvka, Yosef E.
AU - Mouw, Kent W.
AU - Karlic, Rosa
AU - Parasuraman, Prasanna
AU - Kamburov, Atanas
AU - Polak, Paz
AU - Haradhvala, Nicholas J.
AU - Hess, Julian M.
AU - Rheinbay, Esther
AU - Brody, Yehuda
AU - Koren, Amnon
AU - Braunstein, Lior Z.
AU - D'Andrea, Alan
AU - Lawrence, Michael S.
AU - Bass, Adam
AU - Bernards, Andre
AU - Michor, Franziska
AU - Getz, Gad
N1 - Publisher Copyright:
© 2017 Nature America, Inc.
PY - 2017/10/1
Y1 - 2017/10/1
N2 - Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the form of insertions or deletions (indels) of the repeated motif. Despite their prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to difficulties in detecting them in short-read sequencing data. Here we present two tools: MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance. Applying MSMuTect to whole-exome data from 6,747 human tumors representing 20 tumor types, we identified >1,000 previously undescribed MS indels in cancer genes. Additionally, we demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite-stable tumors from tumors with microsatellite instability, thus potentially improving classification of clinically relevant subgroups. Finally, we identified seven MS indel driver hotspots: Four in known cancer genes (ACVR2A, RNF43, JAK1, and MSH3) and three in genes not previously implicated as cancer drivers (ESRP1, PRDM2, and DOCK3).
AB - Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the form of insertions or deletions (indels) of the repeated motif. Despite their prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to difficulties in detecting them in short-read sequencing data. Here we present two tools: MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance. Applying MSMuTect to whole-exome data from 6,747 human tumors representing 20 tumor types, we identified >1,000 previously undescribed MS indels in cancer genes. Additionally, we demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite-stable tumors from tumors with microsatellite instability, thus potentially improving classification of clinically relevant subgroups. Finally, we identified seven MS indel driver hotspots: Four in known cancer genes (ACVR2A, RNF43, JAK1, and MSH3) and three in genes not previously implicated as cancer drivers (ESRP1, PRDM2, and DOCK3).
UR - http://www.scopus.com/inward/record.url?scp=85031106017&partnerID=8YFLogxK
U2 - 10.1038/nbt.3966
DO - 10.1038/nbt.3966
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C2 - 28892075
AN - SCOPUS:85031106017
SN - 1087-0156
VL - 35
SP - 951
EP - 959
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 10
ER -